Would You Rather...

I would certainly go for the rarer year, but the only reason I say this is that I'm not particularly fond of super high grade coins, I collect coins for the history, so I like my coins worn, but with details visible. My favorite grade for a coin is probably VF-20.

I'd rather have a rare coin to complete my set, than a empty hole.

To me it's almost the same in principle, but the specific figures are different; I don't really care much about differences in grades above AU-50 or so - they're all "uncirculated" to me (if anything, the low MS grades are worse).
[I also have nowhere to store high-grade coins, but that goes hand in hand with not having that kind of money anyway.]
My favorite grade for a coin is probably around XF-40 (though I'd probably still prefer a coin in AU over the same coin in XF if the monetary value was similar).

So out of the OP's coins, I'd rather take the rarity, but if I really had that sort of money, I'd much rather buy an AU-58 (or AU-55) 1838 for $1000 (or slightly less), and spend the remaining $5000 on several thousand other cool coins

Yep, rarer coin for sure because the opportunities are rarer too.